Chloroplast DNA (cpDNA) variability and phylogeny were studied via analysis of restriction site mutations and DNA sequencing in a complex of three closely related species of pines: Pinus radiata D. Don, P. attenuata Lemm., and muricata D. Don. Genomic DNA from 384 trees representing 20 populations in the complex were digested with 20 restriction enzymes and probed with cloned cpDNA fragments from Douglas-fir that comprise 85% of the chloroplast genome. Using five trees to represent each major genetic group in the complex, 667 bp of the intergenic region between the chloroplast genes rbcL and atpB were amplified via the polymerase chain reaction and directly sequenced. No variation was observed in the sequenced intergenic region. 313 restriction sites were surveyed, accounting for 1.5% of the chloroplast genome. Twenty-four variable restriction site mutations were observed in the complex. Genetic diversity was nearly confined to differences among species; nucleotide diversity among species was estimated to be 0.3% (±0.09%). Monterey and knobcone pines displayed almost no genetic variation within or among populations. Bishop pine showed strong population differentiation, a result of differences among three geographic groups, but almost no variability within populations (G[subscript]ST) = This pattern of genetic architecture contrasts with that found in a recent allozyme study of the complex, and that of nuclear gene diversity in outcrossing species generally. Factors contributing to this difference are discussed, and may include smaller effective population sizes enhancing genetic drift, lower mutation rates, and periodic (natural) selection of organelle genes. Regions of the genome subject to length mutations were observed, as well as a heteroplasmic individual and a major genome inversion. Phylogenetic analysis of restriction site differences by several methods showed that the three species were distinct, and that bishop and Monterey pines were most closely related. Knobcone pine was closest to the outgroup species, P. oocarpa Schiede, and appeared to have diverged earliest. The relationships of the three geographic groups of Bishop pine indicated a south to north migration along coastal California.